Transcriptomic profile of single-cell sorted CD14+ monocytes from 6 PBMC samples of individuals with active tuberculosis

Previous studies suggest that monocytes are an important contributor to tuberculosis (TB)-specific immune signatures in blood. Here we carried out single-cell profiling of classical CD14+CD16- and intermediate CD14+CD16+ monocytes in paired blood samples of active TB (ATB) patients at diagnosis and end-treatment. At diagnosis, ATB patients displayed upregulation of interferon signaling genes that significantly overlapped with previously reported blood TB signatures in both CD14+ subsets. In ATB diagnosis, we identified additional transcriptomic and functional changes in intermediate CD14+CD16+ monocytes, such as the upregulation of inflammatory and MHC-II genes, and increased capacity to activate T cells, reflecting overall increased activation in this population. Single-cell transcriptomics revealed that distinct subsets of intermediate CD14+CD16+ monocytes were responsible for each gene signature, indicating significant functional heterogeneity within this population. Finally, we observed that transcriptomic changes in CD14+ monocytes were transient, as they were no longer observed in the same ATB patients mid-treatment, suggesting they are associated with disease resolution. Overall design: Single-cell RNA sequencing of sorted CD14+ monocytes from 6 PBMC samples of individuals with active tuberculosis (4 samples at diagnosis, 2 paired samples at end of treatment, 6 months after diagnosis). Each sample was stained with a distinct Total-seq antibody prior sorting for hashtag demultiplexing post-sequencing.